assoc.plink: Perform a genome-wide association scan with PLINK

In andrewparkermorgan/argyle: Basic interface and QC for genotypes from Illumina Infinium arrays

Description

Perform a genome-wide association scan with PLINK

Usage

assoc.plink(prefix, model = c("assoc", "linear", "logistic"),
  test = c("additive", "genotypic", "hethom", "dominant", "recessive"),
  perms = TRUE, nperms = 1e+05, geno.missing = 0, ind.missing = 0,
  maf = 0, hwe = 1,
  flags = "--keep-allele-order --allow-no-sex --nonfounders", ...)

Arguments

prefix	a pointer to a PLINK fileset (of class plink)
model	statistical model for association between genotype and phenotype ("assoc" for case-control contingency table; "linear" for linear model on quantitative trait; "logistic" for case-control logistic regression)
test	family of hypothesis test(s) to perform
perms	logical: establish significance thresholds using adaptive permutation, or skip it?
nperms	integer; maximum number of permutations
geno.missing	drop markers with call rate lower than this threshold
ind.missing	drop samples with call rate lower than this threshold
maf	drop markers with minor-allele frequency lower than this threhsold
hwe	drop markers p-value less than this threshold for test of Hardy-Weinbery equilibrium
flags	additional command-line flags passed directly to PLINK call
...	ignored

Details

See the relevant PLINK documentation for details of the underlying calculations. Note that PLINK doesn't perform kinship correction. There now exists other, smarter software for GWAS including EMMAX, FastLMM and LIMIX.

Value

a dataframe with association results, having the following columns:

• chr

• pos

• marker

• A1 – reference allele (interpretation depends on dataset)

• p.value – p-value for hypothesis test

• OR – odds ratio (in case-control context)

• n – count of non-missing genotypes at this marker

• test – which family of hypothesis test this is

• p.value.perm – empirical p-value from permutations, if applicable

References

PLINK v1.9: https://www.cog-genomics.org/plink2

Purcell S et al. (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 81(3): 559-575. doi:10.1086/519795.

andrewparkermorgan/argyle documentation built on May 10, 2019, 11:08 a.m.